1. 13 Text Processing
Hongfei Yan
June 1, 2016

2. Contents 01 Python Primer (P2-51)
02 Object-Oriented Programming (P57-103)
03 Algorithm Analysis (P )
04 Recursion (P )
05 Array-Based Sequences (P )
06 Stacks, Queues, and Deques (P )
07 Linked Lists (P )
08 Trees (P )
09 Priority Queues (P )
10 Maps, Hash Tables, and Skip Lists (P )
11 Search Trees (P )
12 Sorting and Selection (P )
13 Text Processing (P )
14 Graph Algorithms (P )
15 Memory Management and B-Trees (P )
ISLR_Print6

3. Contents
13.1 Abundance of Digitized Text 13.2 Pattern-Matching 13.3 Dynamic Programming 13.4 Text Compression and the Greedy Method 13.4 Tries

4. Pattern Matching
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13.2 Pattern Matching

5. Strings A string is a sequence of characters Examples of strings:
Python program
HTML document
DNA sequence
Digitized image
An alphabet S is the set of possible characters for a family of strings
Example of alphabets:
ASCII
Unicode
{0, 1}
{A, C, G, T}
Let P be a string of size m
A substring P[i .. j] of P is the subsequence of P consisting of the characters with ranks between i and j
A prefix of P is a substring of the type P[0 .. i]
A suffix of P is a substring of the type P[i ..m - 1]
Given strings T (text) and P (pattern), the pattern matching problem consists of finding a substring of T equal to P
Applications:
Text editors
Search engines
Biological research

6. Brute-Force Pattern Matching
Algorithm BruteForceMatch(T, P)
Input text T of size n and pattern P of size m
Output starting index of a substring of T equal to P or if no such substring exists
for i  0 to n - m
{ test shift i of the pattern }
j  0
while j < m  T[i + j] = P[j]
j  j + 1
if j = m
return i {match at i}
else
break while loop {mismatch}
return -1 {no match anywhere}
The brute-force pattern matching algorithm compares the pattern P with the text T for each possible shift of P relative to T, until either
a match is found, or
all placements of the pattern have been tried
Brute-force pattern matching runs in time O(nm)
Example of worst case:
T = aaa … ah
P = aaah
may occur in images and DNA sequences
unlikely in English text

7. Boyer-Moore Heuristics
The Boyer-Moore’s pattern matching algorithm is based on two heuristics
Looking-glass heuristic: Compare P with a subsequence of T moving backwards
Character-jump heuristic: When a mismatch occurs at T[i] = c
If P contains c, shift P to align the last occurrence of c in P with T[i]
Else, shift P to align P[0] with T[i + 1]
Example
Pattern Matching

8. Last-Occurrence Function
Boyer-Moore’s algorithm preprocesses the pattern P and the alphabet S to build the last-occurrence function L mapping S to integers, where L(c) is defined as
the largest index i such that P[i] = c or
-1 if no such index exists
Example:
S = {a, b, c, d}
P = abacab
The last-occurrence function can be represented by an array indexed by the numeric codes of the characters
The last-occurrence function can be computed in time O(m + s), where m is the size of P and s is the size of S c a b d
L(c) 4 5 3 -1

9. The Boyer-Moore Algorithm
Case 1: j  1 + l
Algorithm BoyerMooreMatch(T, P, S)
L  lastOccurenceFunction(P, S )
i  m - 1
j  m - 1
repeat
if T[i] = P[j]
if j = 0
return i { match at i }
else
i  i - 1
j  j - 1
{ character-jump }
l  L[T[i]]
i  i + m – min(j, 1 + l)
until i > n - 1
return -1 { no match }
Case 2: 1 + l  j
In the case of Figure 13.3(b), we slide the pattern only one unit. It would
be more productive to slide it rightward until finding another occurrence of mismatched
character T[i] in the pattern, but we do not wish to take time to search for

10. Example

11. Analysis Boyer-Moore’s algorithm runs in time O(nm + s)
Example of worst case:
T = aaa … a
P = baaa
The worst case may occur in images and DNA sequences but is unlikely in English text
Boyer-Moore’s algorithm is significantly faster than the brute-force algorithm on English text

12. Python Implementation

13. The KMP Algorithm
Knuth-Morris-Pratt’s algorithm compares the pattern to the text in left-to-right, but shifts the pattern more intelligently than the brute- force algorithm.
When a mismatch occurs, what is the most we can shift the pattern so as to avoid redundant comparisons?
Answer: the largest prefix of P[0..j] that is a suffix of P[1..j] . . a b a a b x . . . . . a b a a b a j a b a a b a
No need to
repeat these
comparisons
Resume
comparing
here

14. KMP Failure Function
Knuth-Morris-Pratt’s algorithm preprocesses the pattern to find matches of prefixes of the pattern with the pattern itself
The failure function F(j) is defined as the size of the largest prefix of P[0..j] that is also a suffix of P[1..j]
Knuth-Morris-Pratt’s algorithm modifies the brute-force algorithm so that if a mismatch occurs at P[j]  T[i] we set j  F(j - 1) j 1 2 3 4 5
P[j] a b
F(j)

15. The KMP Algorithm
The failure function can be represented by an array and can be computed in O(m) time
At each iteration of the while-loop, either
i increases by one, or
the shift amount i - j increases by at least one (observe that F(j - 1) < j)
Hence, there are no more than 2n iterations of the while-loop
Thus, KMP’s algorithm runs in optimal time O(m + n)
Algorithm KMPMatch(T, P)
F  failureFunction(P)
i  0
j  0
while i < n
if T[i] = P[j]
if j = m - 1
return i - j { match }
else
i  i + 1
j  j + 1
if j > 0
j  F[j - 1]
return -1 { no match }

16. Computing the Failure Function
The failure function can be represented by an array and can be computed in O(m) time
The construction is similar to the KMP algorithm itself
At each iteration of the while-loop, either
i increases by one, or
the shift amount i - j increases by at least one (observe that F(j - 1) < j)
Hence, there are no more than 2m iterations of the while-loop
Algorithm failureFunction(P)
F[0]  0
i  1
j  0
while i < m
if P[i] = P[j]
{we have matched j + 1 chars}
F[i]  j + 1
i  i + 1
j  j + 1
else if j > 0 then
{use failure function to shift P}
j  F[j - 1]
else
F[i]  0 { no match }

17. Example j 1 2 3 4 5
P[j] a b c
F(j)

18. Python Implementation

19. The Greedy Method and Text Compression
Merge Sort
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The Greedy Method and Text Compression

20. The Greedy Method Technique
The greedy method is a general algorithm design paradigm, built on the following elements:
configurations: different choices, collections, or values to find
objective function: a score assigned to configurations, which we want to either maximize or minimize
It works best when applied to problems with the greedy- choice property:
a globally-optimal solution can always be found by a series of local improvements from a starting configuration.

21. Text Compression
Given a string X, efficiently encode X into a smaller string Y
Saves memory and/or bandwidth
A good approach: Huffman encoding
Compute frequency f(c) for each character c.
Encode high-frequency characters with short code words
No code word is a prefix for another code
Use an optimal encoding tree to determine the code words
Greedy Method

22. Encoding Tree Example
A code is a mapping of each character of an alphabet to a binary code-word
A prefix code is a binary code such that no code-word is the prefix of another code- word
An encoding tree represents a prefix code
Each external node stores a character
The code word of a character is given by the path from the root to the external node storing the character (0 for a left child and 1 for a right child) a b c d e 00
010
011 10 11 a b c d e

23. Encoding Tree Optimization
Given a text string X, we want to find a prefix code for the characters of X that yields a small encoding for X
Frequent characters should have long code-words
Rare characters should have short code-words
Example
X = abracadabra
T1 encodes X into 29 bits
T2 encodes X into 24 bits c a r d b T1 a c d b r T2
Greedy Method

24. Huffman’s Algorithm
Given a string X, Huffman’s algorithm construct a prefix code the minimizes the size of the encoding of X
It runs in time O(n + d log d), where n is the size of X and d is the number of distinct characters of X
A heap-based priority queue is used as an auxiliary structure
Greedy Method

25. Huffman’s Algorithm